Father Knows Best
by Jamielordofgingers
Summary: Gendo Ikari had run away from a lot in his lifetime. Family, school, jobs, the law, paternity suits... far too much for one man alone. Now, in the shadow of Yui's death, he is tripped up by her son. With Shinji and Rei in hand, the path to Rebirth becomes clearer... if the city of Tokyo-3 can withstand the Destruction first that is.
1. Wanting Nails

Father Knows Best: An Evangelion Fanfiction

**AN:** I'm pretty sure this idea has been done before. I'm certain it's never been brought to completion. Let's change that.

* * *

Chapter One: Wanting Nails

Yui was dead.

A thousand other thoughts should have been his focus at the moment, but it all kept looping back around that. Yui was dead. Kind, smart, benevolent, too-good-for-this-sinful-earth, and certainly too good for him Yui was gone, vanishing into Unit-01, with no chance of returning, despite his efforts, and a litany of curses hurled at Drs Akagi and Fuyutsuki. He couldn't even figure out who to blame. Was it a SEELE plot, or Yui's own design? Assassination or set-up for a grander plan he could only guess at? Maybe it was Fate, a random occurrence or simply just an accident. Gendo was favouring spite right now. Clearly God, or whatever was close to it, had chosen to give its favourite chew toy another kick, just when he'd finally become settled, happy even, with the life he'd forged for himself. Speaking of which…

Settled in his lap, Yui's child gave a kick, eyelids flickering rapidly as he dreamed. To be honest, it was more likely a nightmare. Watching one's mother die before your eyes would do that. Hopefully he would forget it soon, as children were wont to do at his age, and go back to… doing whatever it was his son did. Which probably involved Yui, as God knew Gendo Ikari was not good with children, especially his own. Or anyone other than… dead. She was still dead. Fuck.

But the fact remained. Even with Yui gone, Third Impact would happen, one way or the other, with the members of SEELE becoming the immortal rulers of whatever was left of mankind after that whole clusterfuck went down… they were going to stop it once. Take back mankind from the old men and save the world… or was the plan to help all men ascend to that state prophesized as "Heaven"? Damn it all, would the struggle even be worth it without her? Unless…

But that would be turning his back on everything she had stood for. It might even end up making him as bad as the old men if handled incorrectly… well; it wasn't like he hadn't stared into the abyss before. Hell, it was almost getting to become a hobby. On his lap, the boy yawned, shifting into the palm preventing him from slipping onto the floor head-first. Which brought Gendo back to his other problem. He had no idea how to raise a child, hell, he could barely deal with other people, despite Yui's best attempts to pull him out of his shell. And history had an unfortunate habit of repeating. Could the world really deal with two Gendo Ikaris? The thought sent a shiver up his spine, as unwanted memories came unbidden from the back of his mind.

The shadow looming over him, bottle in hand and malice in eyes.

The stares of other children, hushed whispers in hallways and a sea of backs wherever he would turn.

The gangly teenager built like steel wire, glaring back at him with dead eyes from a broken mirror.

A mix of a hundred unimportant faces, features blurred by alcohol as his fists flew with reckless abandon.

Yui, standing at the mouth of an alleyway looking down on him as shafts of morning sunlight enveloped her form.

If he chose to raise Yui's son, the long path to bringing her back would become longer. He would have to become better than he was… actually try to form bonds with another person, whilst keeping the boy on the straight and narrow, making sure he grew up ready for the trials that lay before humanity. He'd be an Evangelion Pilot, of that there could be no doubt. Unit 01 would probably only respond to him now, if they were unlucky. And Lady Luck hadn't so much as glanced his way in years.

Or, he could ship him off to Yui's sister and her family. Better to have no father than one who could barely care for himself, let alone a child. Her branch of the family had never seen eye-to-eye with him, but they would take in his nephew without complaint. It would likely be a cold household, and it risked the boy growing up to be anything, perhaps even something out of Gendo's control. But it would be easier. He could once again become the man with a heart of stone without the boy with Yui's features looking at him every day.

"Dad? Is Momma back?"

Shit, when did he wake up? Hesitantly, he rested his free hand on the boy's head, staring into those hopeful, dark blue eyes, one of the few things he inherited from his father. And now he had to break the news to the child he himself was barely recovering from.

"Your mother isn't returning Shinji… she's gone."

There, clear and to the point. That should get it across well enou- oh god, please don't start crying!

"Gon'?"

"Yes… yes, she is."

And so began the waterworks, the child resting his head into Gendo's chest and howling as he left a trail of tears and snot across his sweater, arms wrapped tightly around his father. Damn, would he be able to deal with a lifetime of this? Raising a child that felt more his wife's than his own, struggling through the pain of her disappearance, trying to fill the gap left behind by someone undoubtedly his better? Yes, abandoning him would be best; he would only be hurt if he stayed in the presence of his father. He'd make some calls, gather up his things and take him over on the train before the week was out.

The crying had come down to a most suitable level as the child dissolved into sniffles, before looking back up at his father, probably expecting his tears to be wiped away by a caring hand.

"Can she come bac'?"

Stop. Stop staring at him with those expectant eyes, like your father is worth a damn and can make this better without sacrificing the rest of the planet. Stop looking like her, twisting the knife in his heart with each word. Stop… stop making him reconsider throwing you to the wolves for your own good.

"Dad?"

… It would be useful to have a trained pilot, especially one with undying loyalty to his father. One who could help stand with him as they attempted to bring back his mother, and fight the old men. It wasn't like there were many other candidates after all. And, if he did have to call him back to Toyko-3, wouldn't it be better if he could protect himself? He'd still be throwing Yui's son out to fight monsters from beyond the realm of human understanding, but at least he'd be able to match them.

"Maybe."

Why did you say that? What part of you possessed you to say that? This will end terribly, it could never end well!

Still… if he could form a bond with one Ikari, who wasn't to say he couldn't do it again? He was going to attempt the impossible anyway, why not go beyond it and reforge himself in the seas of parenthood whilst he was at it?

Damn, Yui had changed him more than he'd thought; this sort of optimism, however stumbling and shaky, was unknown to him before. Biting on his lip with a resigned sigh and a prayer to whatever God existed to be kind to him for a second time in his life; he scooped up the child and made for the door of his office.

"Come on Shinji, let's find Uncle Kozo, we've got work to do."


	2. Rise Up, Young Boy

Father Knows Best: An Evangelion Fanfiction

Chapter 2: Rise Up, Young Boy

The air in the Nerv command centre could be described as sombre at best. On the giant monitors connected to the city's CCTV, the Third Angel was rampaging through downtown Tokyo-3 in a manner befitting a kaiju movie, leaving a trail of death and debris in its wake… and now it was flying. Wonderful. All around, technicians and computers were working nine to the dozen, the steady clicks and whirs providing the standard soundtrack for the military base. Well, that and the squeaking.

Squeak, squeak, squeak, squeak, squeak, squeak.

Squeak, squeak, squeak, squeak, squeak, squeak.

Squeak, squeak, squeak, squeak, squeak, squeak.

"Shinji, I swear to whatever Gods exist that if you don't stop pacing, I'm sending you out there to fight the Angel with a spork!"

The squeaking stopped immediately as The First Child shuffled his way over to Nerv's Tactical Operations Officer, leaning on a metal rail overlooking the vice command centres, where representatives from the JSSDF were struggling in vain to command their forces against the Angel. It was the kind of pair one usually only saw in anime. On the left, a busty older woman dressed in an outfit that seemed more suitable for a night on the town than leading a military outfit, despite the official looking jacket, and a stringy, unassuming boy that couldn't stand out in a crowd, dressed in a skin-tight bodysuit more suited to a fetish club than a military organisation. He folded his arms with a sigh, scanning the room with a lazy eye.

"Sorry Captain, it's just that this waiting is killing me. We're the only organisation with the ability to destroy it, and we're being left hanging in the wind whilst those idiots throw gunship after gunship at it." He gave another soft sigh. "It's such a waste. Not to mention- hurk!"

His speech was cut off as his head was introduced to the Captain's chest by way of headlock, the woman gently rasping her knuckles across his scalp.

"Captain!"

"Aww, you're so cute when you worry."

"Let go!"

"Say my name boy!"

"Captain!"

"There's no-one here called Captain, First Child!"

"Misato!" Shinji snapped, pulling out from marshmallow hell, face a furious red as he straightened his hair back into place, before reassuming his position, abet a few steps to the left of the officer.

"Why do you have to do that?"

"Being so serious at your age isn't good for you, you know. You'll be grey before you hit twenty-five."

"And besides," and here his superior officer gave him a pout that would have knocked any of the male Nerv staff off their feet, "you don't mind it outside of work."

Shinij's face flushed even darker as he tried to ignore the round of whispers that went around the room between other Nerv staff who had as little as he did to do right now, and new bets drawn up in the office betting pool about exactly how many of the female staff he had seduced. (Actual number: 0, Speculated number: 42, including his own sister, disturbingly enough.) He shifted into as comfortable position as he could on the rail, equally trying to ignore how much his (ridiculously tight) plugsuit showed off to any spectators, muttering something about sexual harassment. Misato Katsuragi had only joined Nerv about five years ago after the collapse of Gehirn, and upon meeting Shinji and his sister, she had fallen into an pseudo-elderly sister role for the two with ease, much to the male pilot's chagrin at times.

"What I was going to say is, why not go see Rei? She's probably a bit lonely in the hospital."

"Even if I did, she probably wouldn't register me. The doctor have her drugged up to the tits on morphine after the third attempt to sneak up here."

"Well, at least she's in good spirits, better than she should be, considering the accident."

Shinji made a non-committal grunt as the pair returned their attentions back to the main viewing screen, as the JSSDF Generals looked up in anticipation, one of them slamming a phone down triumphantly. Taking a moment to read his lips as he sneered at the Supreme Commander, Misato turned back to Shinji.

"Well, the good news is you should probably high-tail it to the Eva cages, I think we'll be called up to bat soon."

"What makes you say that?"

"'Cause if an N2 mine doesn't snuff it, that pretty much just leaves us."

As the pair watched, a bomber roared down on the Angel, unloading its cargo directly into the bird-like mask, before spiralling off into the sky as the cameras went dead from the following EMP shockwave. The Generals looked on, daring to hope that their lives, and the future of the planet, wouldn't be left in the hands of a fourteen year old boy. That hope was quickly robbed from them as the cameras returned, only to reveal hell on earth, with the regenerating Angel standing amongst the flames, dark unworldly flesh melting from its frame as it proclaimed victory over the humans simply by remaining stoically upright.

Control was quickly passed over to Nerv, Supreme Commander Gendo Ikari stalking over to his head pilot and Operations Director.

"You know what to do."

And with a quick nod to the First Child, he ascended to his high chair to resume his place as lord and master of all he surveyed, Fuyutsuki assuming place at his side as was the norm. And with that, Shinji turned to Misato with a determined grin firmly on his face.

"Well Captain, ready for some revenge by proxy?"

Misato's smile was less confidant, and a little shaky, but she clapped the boy on the shoulders regardless.

"Let's go get it."

Maybe he should have gotten in the plug sooner. As it was, the Nerv teams were running through every last minute and preparation as the Angel loomed closer to their location. As such, he was left here waiting on the LCL to flood the cockpit. The LCL wasn't so much the problem, other than the knowledge he'd be hacking it back up later. It was the thought that there may not be a later that was plaguing him. He was the last line of defence. If he went down, humanity went with him. The Geofront, Japan, the entire world – gone if he fucked this up. Maybe he shouldn't have been so eager to fight, now the pressure was killing him instead of boredom.

"You're going to be alright Shinji. It's not like we're throwing you into this without training or help. Everyone's behind you, so kick that alien git to the curb, and I'll give you special reward when you get back."

It must have been showing on his face real badly if Misato had to intervene. Although, his chest did feel lighter now, enough that he could manage a shaky grin back into the camera.

"I don't know, your rewards always have a habit of backfiring. Remember Rei's twelfth birthday?"

"In my defence, how was I supposed to know she was going to hate clowns? Oh, and we're launching you in thirty seconds, so brace yourself!"

He lent forward, clutching at the butterfly handles as the walls of the plug began their nonsensical multi-coloured lightshow, before settling into combat mode. He could faintly hear the countdown in the background as the nerves began to wind back around in his stomach. Breathing deeply, he returned to his familiar mantra as one of Dr Akagi's assistants announced his synchronisation level of 85.6%, holding steady as it should be. Anything lower would have just been embarrassing.

"_Don't fail them, don't fail them, don't fail them."_

The countdown fell to the last ten digits as he glanced to his father in the background, working on some last minute paperwork, passing it on to his uncle Kozo.

"_Definitely, don't fail him."_

* * *

It was easy to think that the Angel was anything but. After all, it definitely didn't look like the normal cultural image of a winged humanoid. A bird-like mask growing under the original face of the creature contrasted the slick, dark green skin on a loping, hunched body, with huge bony shoulders that look more like pauldrons that body parts, with each hand ending in three fingers. Still, history would judge whether it or the giant purple robot that was glaring down at it looked more like a Godzilla movie reject, the mask twisting to one side at a 45 degree angle as the Evangelion was released from its clamps. The silence was deafening as it took a proud step forward, before a young voice sounded out across the city, despite the mouth not being visible or moving.

"Hi there! Welcome to Tokyo-3. I'm Shinji Ikari, this is Evangelion Unit-01. We're the welcoming-"

BOOM!

The almighty burst of light and heat cut off whatever was being said as a great cross coated the streets in flame. More than one heart caught in the chests of the Nerv staff as the city went silent once again.

Only for the crowd to roar in approval as Unit-01 vaulted over a shopping centre to plant both feet in a solid dropkick, smashing the Angel between the eyes, the AT field shattering as if it wasn't even a factor, the momentum carrying the giant robot forward, grinding the alien's back down the concrete before unleashing a vicious punch to the right shoulder, cracking the bone with one hit as they ground to a halt. Without pause, the Angel's leg shot back up to kick Unit-01 forward, sending it into a forward roll, landing next to an armament building. Snatching up a tank sized revolver, the Eva fired a three round burst as the Angel staggered to its feet, before unleashing another blinding cross of light down the city, charging back into the fray as Unit-01 pulled itself up again from it's evasive roll, hitting it with a clothesline with the rubbery left arm, snatching the head with the other in a quick second movement, before plunging a beam of light straight through the skull of humanity's champion. Watching as the robot went limp, the Angel discarded it with distain, hurling it away across the city with the effort of a public litterer.

* * *

"Shinji! Shinji, respond!"

The cameras in the command centre had once again gone dark, and the power timer had begun to make its relentless countdown. Misato was pounding at a console with abandon, as if whacking it enough times would revive the connection. Above her, Gendo and Fuyutsuki observed with calm temperament.

"You think she'll appear?"

"Not yet. He's not suffered enough."

"It almost sounds like you want him to lose. Not exactly a good show of fatherhood Ikari."

Beneath his gloves, Gendo allowed himself a rare smile.

"Of course, that implies that Shinji would ever allow himself to lose."

* * *

_"Okay, note to self. Taunt the Eldritch Abomination from_ beyond_ the farthest of mankind's understanding after you've killed it."_

Pain lanced through his eye and up his back where Unit-01 had landed on a building. The countdown had begun, which meant his mission had just become twice as hard. Biting down on his tongue, Shinji forced himself through the pain. He wasn't going out this early, not like this. Unit-01 began to rumble to its feet, shaking the remains of the apartments away as its one good eye watched the Angel pad towards the centre of the city. Three minutes and one eye. Well, no-one ever said this would be easy.

Bracing itself against the earth, Unit-01 kicked off like an Olympic runner, charging at its destined enemy. Clearing streets in great bounds, the giant robot continued the charge as the Angel turned to face the noise, right eye glaring into light to fire the cross once more. It wasn't hitting a third time, as Unit-01 launched itself into the air, flames skirting the legs as it crashed down into the Angel with a double-handed hit from a laced fist into the shoulder, breaking it open and twisting the limb backwards with a sickening _CRACK! _of broken bone.

"One!"

A brutal left punch, cracking the core and sending the creature reeling in pain and anger.

"Two!"

Both hands grabbed the throat of the monster, forcing it to its knees as the horned helm plunged down, shattering the skull with one almighty headbutt, shards raining to the streets below.

"Three!"

As the left hand continued its relentless chokehold, the right snapped up to grab the Progressive knife from the shoulder fin, the counter running into two minutes as the weapon was plunged into the breach in the core, sparks screaming from the point of contact as the Angel screamed defiance, limbs flailing in a vainglorious attempt to break free. Gritting his teeth, Shinji forced his will forward, dragging the Angel into the air as Unit-01 once again began the unforgiving drive forward, continuing to press the knife into the heart of the creature. Where to put it down? Ah, there would do nicely.

As the staff of Nerv looked on, Unit-01 began leading the Angel to a large crossroads, away from most of the residential buildings as it ignored the repeated knee strikes to the groin. Really now, that was just getting petty.

"As I was saying!"

Unit-01 forced the Angel higher once more, before slamming it down in the centre of the crossroads as the neck snapped, the remains of the bird skull hanging loose as the knife completed its path into the core with a damning THUNK as the hilt hit the shell. With a final twitch of the gangly limbs, the Third Angel fell still. Unit-01 rose up once again, planting foot onto the knife and baring down on the alien corpse.

"I'm Shinji Ikari, this is Evangelion Unit-01! Welcome to Tokyo-3, Bitch!"


End file.
